The British project could make complex operations safer, New Scientist magazine reports.
It relies on a combination of scans and massive computing power to predict how the brain's blood vessels will respond to surgery.
The University College London team said the simulation could one day spot those at highest risk of a fatal aneurysm.
The brain is supplied by a complex tangle of tiny blood vessels, and a surgeon who wants to deal with an abnormality must navigate through these.
If the wrong vessel is damaged, the result can be a stroke, or even death.
Advanced techniques, such as rotational 3D angiography, are used to create a three-dimensional "map" of these vessels.
However, the latest technique tries to predict in advance what will happen to the blood pressure and flow in other parts of the network if the surgeon has to block off certain blood vessels to complete the operation.
A handful of pressure readings taken from a catheter in a main blood vessel are fed into the computer modelling software, which then makes up to a trillion calculations per second to calculate blood flow changes in the rest of the brain.
This requires vast computing power, and the project, run jointly between UCL and Manchester and Edinburgh Universities, will need access to a network of 20 supercomputers in the US and UK.
Dr Stefan Brew, one of the researchers, said: "What we are trying to do is work out is a way to minimise problems.
"At the moment we tend to not have an accurate picture of what will happen if we interfere with the blood supply."
Aneurysm hope
He said that in future, the system might have wider applications, such as predicting the danger posed by brain aneurysms, bulges in blood vessels caused by a weakening of their structure.
One in hundred people have one, but only 1% of these will rupture, will devastating consequences.
Brain surgery to correct aneurysm can also cause rupture, so the technology could in theory be used to predict which aneurysms pose the greatest threat, so only those at risk receive operations, said Dr Brew.
"If we could achieve that, it would be a major breakthrough," he added.
Dr Andrew Clifton, a consultant neuroradiologist from St George's Hospital in London, said that while neurosurgeons did have techniques to minimise the risk to patients, the research was "potentially useful".
He said: "It seems like 'work in progress' at present, and so I would not expect to see it in operating theatres within the next few years.
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